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Salvia WS, Mantel G, Saha NK, Rajawasam CWH, Konkolewicz D, Hartley CS. Controlling carbodiimide-driven reaction networks through the reversible formation of pyridine adducts. Chem Commun (Camb) 2024; 60:12876-12879. [PMID: 39403777 DOI: 10.1039/d4cc03633f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2024]
Abstract
Carbodiimides and pyridines form reversible adducts that slowly deliver carbodiimide "fuels" to out-of-equilibrium reaction networks, slowing activation kinetics and elongating transient state lifetimes. More-nucleophilic pyridines give more adduct under typical conditions. This approach can be used to extend the lifetimes of transient polymer hydrogels.
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Affiliation(s)
- William S Salvia
- Department of Chemistry and Biochemistry, Miami University, 651 E. High St., Oxford, OH 45056, USA.
| | - Georgia Mantel
- Department of Chemistry and Biochemistry, Miami University, 651 E. High St., Oxford, OH 45056, USA.
| | - Nirob K Saha
- Department of Chemistry and Biochemistry, Miami University, 651 E. High St., Oxford, OH 45056, USA.
| | - Chamoni W H Rajawasam
- Department of Chemistry and Biochemistry, Miami University, 651 E. High St., Oxford, OH 45056, USA.
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E. High St., Oxford, OH 45056, USA.
| | - C Scott Hartley
- Department of Chemistry and Biochemistry, Miami University, 651 E. High St., Oxford, OH 45056, USA.
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Späth F, Soria-Carrera H, Stasi M, Sastre J, Kriebisch BAK, Boekhoven J. Fuel-Driven Dynamic Combinatorial Peptide Libraries. Angew Chem Int Ed Engl 2024; 63:e202407424. [PMID: 39073290 DOI: 10.1002/anie.202407424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024]
Abstract
Dynamic combinatorial chemistry (DCC) creates libraries of molecules that are constantly interchanging in a dynamic combinatorial library. When a library member self-assembles, it can displace the equilibria, leading to emergent phenomena like its selection or even its replication. However, such dynamic combinatorial libraries typically operate in or close to equilibrium. This work introduces a new dynamic combinatorial chemistry fueled by a catalytic reaction cycle that forms transient, out-of-equilibrium peptide-based macrocycles. The products in this library exist out of equilibrium at the expense of fuel and are thus regulated by kinetics and thermodynamics. By creating a chemically fueled dynamic combinatorial library with the vast structural space of amino acids, we explored the liquid-liquid phase separation behavior of the library members. The study advances DCCs by showing that peptide structures can be engineered to control the dynamic library's behavior. The work paves the way for creating novel, tunable material systems that exhibit emergent behavior reminiscent of biological systems. These findings have implications for the development of new materials and for understanding life's chemistry.
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Affiliation(s)
- Fabian Späth
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Héctor Soria-Carrera
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Michele Stasi
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Judit Sastre
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Brigitte A K Kriebisch
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Job Boekhoven
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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Saha NK, Salvia WS, Konkolewicz D, Hartley CS. Transient Covalent Polymers through Carbodiimide-Driven Assembly. Angew Chem Int Ed Engl 2024; 63:e202404933. [PMID: 38772695 DOI: 10.1002/anie.202404933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/23/2024]
Abstract
Biochemical systems make use of out-of-equilibrium polymers generated under kinetic control. Inspired by these systems, many abiotic supramolecular polymers driven by chemical fuel reactions have been reported. Conversely, polymers based on transient covalent bonds have received little attention, even though they have the potential to complement supramolecular systems by generating transient structures based on stronger bonds and by offering a straightforward tuning of reaction kinetics. In this study, we show that simple aqueous dicarboxylic acids give poly(anhydrides) when treated with the carbodiimide EDC. Transient covalent polymers with molecular weights exceeding 15,000 are generated which then decompose over the course of hours to weeks. Disassembly kinetics can be controlled using simple substituent effects in the monomer design. The impact of solvent polarity, carbodiimide concentration, temperature, pyridine concentration, and monomer concentration on polymer properties and lifetimes has been investigated. The results reveal substantial control over polymer assembly and disassembly kinetics, highlighting the potential for fine-tuned kinetic control in nonequilibrium polymerization systems.
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Affiliation(s)
- Nirob K Saha
- Department of Chemistry and Biochemistry, Miami University, 651 E High St, Oxford, OH, 45056, United States
| | - William S Salvia
- Department of Chemistry and Biochemistry, Miami University, 651 E High St, Oxford, OH, 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E High St, Oxford, OH, 45056, United States
| | - C Scott Hartley
- Department of Chemistry and Biochemistry, Miami University, 651 E High St, Oxford, OH, 45056, United States
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Zozulia O, Kriebisch CME, Kriebisch BAK, Soria-Carrera H, Ryadi KR, Steck J, Boekhoven J. Acyl Phosphates as Chemically Fueled Building Blocks for Self-Sustaining Protocells. Angew Chem Int Ed Engl 2024; 63:e202406094. [PMID: 38743852 DOI: 10.1002/anie.202406094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/21/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Lipids spontaneously assemble into vesicle-forming membranes. Such vesicles serve as compartments for even the simplest living systems. Vesicles have been extensively studied for constructing synthetic cells or as models for protocells-the cells hypothesized to have existed before life. These compartments exist almost always close to equilibrium. Life, however, exists out of equilibrium. In this work, we studied vesicle-based compartments regulated by a non-equilibrium chemical reaction network that converts activating agents. In this way, the compartments require a constant or periodic supply of activating agents to sustain themselves. Specifically, we use activating agents to condense carboxylates and phosphate esters into acyl phosphate-based lipids that form vesicles. These vesicles can only be sustained when condensing agents are present; without them, they decay. We demonstrate that the chemical reaction network can operate on prebiotic activating agents, opening the door to prebiotically plausible, self-sustainable protocells that compete for resources. In future work, such protocells should be endowed with a genotype, e.g., self-replicating RNA structures, to alter the protocell's behavior. Such protocells could enable Darwinian evolution in a prebiotically plausible chemical system.
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Affiliation(s)
- Oleksii Zozulia
- Department of Bioscience School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Christine M E Kriebisch
- Department of Bioscience School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Brigitte A K Kriebisch
- Department of Bioscience School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Héctor Soria-Carrera
- Department of Bioscience School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Kingu Rici Ryadi
- Department of Bioscience School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Juliana Steck
- Department of Bioscience School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Job Boekhoven
- Department of Bioscience School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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Ranganath VA, Maity I. Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises. Angew Chem Int Ed Engl 2024; 63:e202318134. [PMID: 38226567 DOI: 10.1002/anie.202318134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.
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Affiliation(s)
- Vinay Ambekar Ranganath
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
| | - Indrajit Maity
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
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Zwick P, Troncossi A, Borsley S, Vitorica-Yrezabal IJ, Leigh DA. Stepwise Operation of a Molecular Rotary Motor Driven by an Appel Reaction. J Am Chem Soc 2024; 146:4467-4472. [PMID: 38319727 PMCID: PMC10885133 DOI: 10.1021/jacs.3c10266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
To date, only a small number of chemistries and chemical fueling strategies have been successfully used to operate artificial molecular motors. Here, we report the 360° directionally biased rotation of phenyl groups about a C-C bond, driven by a stepwise Appel reaction sequence. The motor molecule consists of a biaryl-embedded phosphine oxide and phenol, in which full rotation around the biaryl bond is blocked by the P-O oxygen atom on the rotor being too bulky to pass the oxygen atom on the stator. Treatment with SOCl2 forms a cyclic oxyphosphonium salt (removing the oxygen atom of the phosphine oxide), temporarily linking the rotor with the stator. Conformational exchange via ring flipping then allows the rotor and stator to twist back and forth past the previous limit of rotation. Subsequently, the ring opening of the tethered intermediate with a chiral alcohol occurs preferentially through a nucleophilic attack on one face. Thus, the original phosphine oxide is reformed with net directional rotation about the biaryl bond over the course of the two-step reaction sequence. Each repetition of SOCl2-chiral alcohol additions generates another directionally biased rotation. Using the same reaction sequence on a derivative of the motor molecule that forms atropisomers rather than fully rotating 360° results in enantioenrichment, suggesting that, on average, the motor molecule rotates in the "wrong" direction once every three fueling cycles. The interconversion of phosphine oxides and cyclic oxyphosphonium groups to form temporary tethers that enable a rotational barrier to be overcome directionally adds to the strategies available for generating chemically fueled kinetic asymmetry in molecular systems.
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Affiliation(s)
- Patrick Zwick
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Axel Troncossi
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Stefan Borsley
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | | | - David A Leigh
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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